unparsable vcf record with allele CTGATTAACCACTTGGAAATT....

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Valentina Andrioletti

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4:20 AM (18 hours ago) 4:20 AM

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Hi all,

I also posted on the IGV repository.

I loaded the VCF on IGV using the hg38 reference genome (as the VCF) and when jumping to the chr3 I received this error:

SEVERE [Dec 12,2025 09:20] [FeatureTrack] htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 1699441: unparsable vcf record with allele CTGATTAACCACTTGGAAATTCTGCAATAAGAGAGTTTCAAAACTGCTCTATGAAAGGAAGGTTCAACTCTGTGAGTTGAAAGCACACGTCACAAAGAAGTTTCTGAGAACTCTTCTGTCTAGTTTTAAATGAAGAAGTCACGTTTCAAACGAAGGCCACAAAGAGGTCCAAATATCCACCAGCAGATTCTATAAAAAGAGTGTTGCGAAACTGCTCTCTCAAGAGGAATGCTCAATTCTGTGTGTTGAATGCAAATATCACAAAATAGTTTCCGACAATGCTTCTGTCAAGTATCTATTTGAAAATATTTCCTTTTCTACCGTAGACTTCAAAGCAGTCTAAATGTACACTTGGATATTCCACAAAATAATGTTTCAAAACTGCTCTATTAAAAGAAACGTTAACATTTGTAAGGTTAATGCACACATCACAAAGTAATTTCTGAAAATGATTCTGTCCAGTTTTTCTATGAAGATATTTCCTTTTCTACCACAGCCTCAAACTGCTGTAAATATCCACCTGGAAATTCTAAAAAAAGAGTGTTTCAAAACTGCTCTATCGAAAGGAAGTTTTAACTCTGTGAGTTGAATGCACACATGACAAAGATGTTTCTGAGAATTCTTCTGTCCAGTTTTATTTGAAGGAATTCCATTTCCAACGCAGACCTCAACAAGTCCAAATATTAACTTGCAGATTCTACAAATAGTGTGTTTCAAAACTGCTCTATCAAAAGAAAGATTAAACTCTGTGAATTGAACGCACACATCACAAAGTAGTTTCAGAGAATCATTCTCTCTAGTTTTCCTATGAAGATATTGCCTTTTCTAAAATTGGCCTCTAACGGTGCTAAATATCCACTAGGAAATTATACAAAAATAGTGTTTCAGAACTGCTCCATACAAAGGAAAGTACAACTCGGTGAGTTGAAAGCACACATCACAAAGAATTTCTGAGAACTATTCTTTCTAGTTTTATATGCAGAAATAACTTTTCAAACGAAGGCCACAAAAAGGTCCAAATATCCACTTGCATATTCTACAAAAAAAGAGTTTCAAAACTGCTCTATGAAGAGCAATGTTCAACACTGTGAGTTGAATGCAAATATTGCGAATTAGTTTCTGACAATGCTTCTGTCTAATTTTTATGTGAAGTTATTTCCTTTTCTACCGTAGGCCTCAAAGCCCTCTGAATGTACACTTCCAAATATCACAAAAAGAGTGTTTCAAAACTGCTCTGTCAAAGGAATGGTTAAACATTGTAAGCTGAATGCACCCATCACAAAGTAGTTTCTGAGAATGATTCTGTCTAGTTTTTTAATGAAAATATTCCCTTTTCAATCATTGGCCTCAAACCACTCAAAATATCCACTTGGAAATTCTACAAAAAGATTATTTCAAAAGTGCTCTATCGAAAGGAAGTTTCGACTCTGTGTGTTGAATGCACACATCACAAAGAAGTTTCTGAGAATTCTTCTGACAAGTCTTATATGAAGAAATCCCATTTCCAAAGAAGGCCTCAAAAAAGTCCAAATATTCACTTGCAGATTCTACAAAAAGATTGTTTCAAAACTGCTCTATCAACAGAAAGGTTAAACCCTTTTGATTTGGACGCACACCTCACAAAGAAGTTTCTGAGAATTCTTCTGTCTAGTTTTATATGAAGAAATCACTTTTCAAAAGAAGGCCACAAGGAGGTCCCAAAATCCCCTTGTAGATTCTACAAAAAGAGTGTTTCAAAACTGCTCTATCAAGAGGAATGTTCAACTCTGTGAGTTGAATGCAAATATCACATAGTAGTTTCTGACAATGCTTCTGTCTAGTTTTTATGTGAAGATATTTCCTTTTCCACCGTAGGCCTCAAAGCACTCAAAATATACACTTGCAATTTCCACAAAAAGAGTGTTTCAAAACTGTTCTATGAAAAGAAAGGTTAAACTCTGTAAGCTGAATGCGCCCATCACAAAGTAGTTTCTGAGAATGATTCTGTCTAGATTTCAATGAAGATATTTCCTTTTCTACCATACGCCTCAAACCGCTCTAAATAATATCCACTTGGAAATTCTACAAAAACAGTACTTCAAAACTGCTCTATGGAAAGGAAGGTTCAACTCTGTGAGTTCAATGCGCACATCACAAAGAAGTGTCTGCGAATTCTTTTGTCAAGTTTTATATGAAGAAATCCCGTTTCCAACTAAGGCCGTAAAAAAGTCCAAATATTCCCTTGCAGATGCTACAAAAAGTGTGTTTCAAAACTGCTCTATCAAAAGAAAGGTTAAATTCTCTGAATTGAACGCAGACATCAAAAAGTAGTTTCTGAGAATCATTCTGTCCAATTTTTTTATGAAGATATTGCCTTCTCTACCATAGGCCTCAAACGGTGCCAAATATACACTGGGAAATCCTAAAAAAAAAGAGAGTGTGAAAACTGCTCCATCGAAAGGAAGTTTCAACCCTTTGAGTTGAAAGCACACATCACAAATATGTTCCTCAGAATTCTTCTGTCTATTTTTATATGAAGAAACCACGTTTCAAAAGTACGCCACAAGGTGGTACAAATATCCACTTGCAGATTCTACAAAAAGAGTGTTTAAAATCTGCTCCATGAAGAAGAATGTTCAACTCTGTGAGTTGAATGCTAATATCACAAAGTAGTTTCTGACAAAGATTCTGTCTAGTTTTTATGTAAAGATATTTCCTTTTCTATCGTAGGCCTCAAATCGCTCTAAATATACACTTGCAATTTCCACAAACAGAGTGTTCCAAAACTGCTCTAAAAAAGAAAGGTTCAACTCTGTGAGCTGAATGCACACATCACAAAGTAGTTTCTGAGAATGATTCTGACTAATTTTTCTTCGCAGATATATCCTTTTCTACTGTACGCCTCAAACGGCTCTAGATATCCACTTGGAAATTCTAAAAAAAGAGTATTTCAAAACTGCTCTATCGAAAGGAAGGTTCAACTCTGTGAGTTGAAAGCACACATCACAAAAAAGTTCCTCACAATTCTTCTGTCTAGTTTTATATGAAGAAATCACTTTTCAAAGGAAGGCCACAAACAGGTCCAAATATCCACTTGTATTTTCTACAAAAAGAGTGTTTCAAACTGCTCTATCAAGAGGAATGTTCAACTCTGTGAGTTGAATGCAAATATCACAAAGTAGTTTCTGACAATGCTTCTGTCTTGTTTTTATGTGAAGATATTACCTTTTCTACAGTAGGCCACAAAGCGCTCTAAATATACACTTGCAAATTCCACAAAAAGAGTGTTTCAAATCTGCTCTATGAAAAGAAAGGTTAAACTCTGTGAGATGAATGCACACATCACAAAGAAGTGTCTGAGAATTCTTCTGACAAGTCCTATATGAAGAAATGCCGTTTCCAATGATGGCCTCAAAAAAGTCCAATTATTCACCTGCAGATTGTACAAAAAGAGTGTTTTCAATACTGCTTCTATAAAGGAAAGGGTAAACTTTGTGCGTTTGAATGCACACATCACAAATAAGTTTCTGAGAATCATTCTCTCTTGTTTTTCTGTGAAGWTATTGCCTTTTCTACCATAGGCCTCAAAAGGGGCTAAATATCCACTTGGATACCCCACTAAAAGAGAGTTTCATAACTGCTGTATCGAAAGGAAGTTTCAGCTCTGTGAGTTGAAAGCACACGTAACAAAGAAAGAAGTTTCTGTGAATTCTTCTGTCTTGTTTTACATGAAGAAATCACGTTTCAAATGAAGGCCACATAGAGGTCCAAATATCCACTTACAGATTCTACAAAAAGAGTGTTTCAGTATTCCTCTATCGAAAGCAAAGTTAAACTCTGTGAGTTGAATACACACATCACAAAGTAGTTTCTGAGAATCATTCTGTCTGGTTTTTCTATGAAGATATTGCCTTTTCTACCATTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTAAACTCTGTGAGTTGAATACACACATCACAAAGTAGTTTCTGAGAATCATTCTGTCTGGTTTTTCTATGAAGATATTGCCTTTTCTACCATAGGCCTCAAATGGCACTAAATATCCACTTGGAAATCCTACAAAAAGAGAGTTTCCAAACTGCTCTATCAAAAGAAAGGTTCAACTCTGAGAGTTGAAATCACACATCACAAAGAAGTTTCTGAGAATTCTTCTGTCCAGTTTTATATGATGAAATCACCTTTCAAAGGAAGGCCACAAAGAAGTCCAAATATCCACTTGCAGATTCTACAAAAATAGTGTTTCAAAACTGCTCTATCAGGAGGAAGGTTCAACTCTGTGAGTTGAATGCCAATATCACAAAGTAGTTTCTGACAATGCTTCTGTCTAGTTTTAATGTGAAGATATTTCCTTTTCTACAGTAGGCCTCAAAGCGCTCTAAATATACACTTGAAAATTCCACAAAAATAGTGTTACAAAACTACTCTACCACAGGAAAGGTTAAACTCTGTAAGCTGAATGCACACATAACTAATTAGTTTCTGAGAATGATTCTGTCTAGGTTTTGTATGAAGATATTTCCTTTTCTTCCATAGGCATCTATCCGCTCTAAATATCCACTTGGAAATCCTACAAAAAGAGTATTCCAAAACTGCTCTATCATAAGGACGGTTCAACTCTCTGGGTTGAACGCACACATGAAAAAGAAGTTTCTGAGAATTCTTCTGCCAAGTTTTATATGAAGAAATGCCGTTTCCAACGAACGCCTCATAAAAGTGTAAATATTCAATTGCAGATTCTGCAAAAAGAGTGTTTTAAAACTGCCGTATGAAAAGAAAGTTTAAATACTGTGAGTTGAACGCACACAGCACAAAGCAGTTTCTGAGTATCATTCTGTCTTGTTTTTATGTGATGATATTTCCTTTTCTACCGTAGGCCTCAAACGGCGCTAAATAGCCACTTGGAAATTCTACAAAAAGAGTATTTCAGAACCGCTCTATCGAAAGGAAGGTTCAACACTGTGAGTTGAAAGCACACATCACAAAGTAGATTCTGATAATTCTTCTGTCAAGTTTTATATGAAGAAACTCCATTTTCAAAAATGGCCTCTAAAAAATCCAAATATTCACTTGCAGATTCTACAAAAAGAGTGTTTAAAAACTGCTCTATCAAAAGAAAGGTTAAACTCTGTGAGTTGAATGCACACATCACAAAGTAGTTTCTGAGAATCTTTCTGTCTAGTTTTTCTATGAAGATACTGCCTTTTATTCCATCGGCCTCAAACGGCGCTAAATATCCACCTGGAAATTCTACAAAAAGAGAGTATCAAAACTGCTCTATCGAAAGAAATGTTCAACACTGTGAGTTGAATGCAGATATCACAAAGTAGTTTCTGACTATGCTTCTGTCTAGTTTTAATGGGAAGATATTTCCTTTTCTACCATAGGCCTCAAAGCGCTCTAAATATACACTTGCAAAGTCCACAAAAAGAGAGTTACAAAACTGATCTATCAAAAGAAAGGTTAAAGTCTGTAAGCTGCATGCACACATTAGAAAGTAGTTTCTGAGAATGATTCTGTCTAGGTTTTCTATGAAGATAATTCCTTCTCTACCACAGGCCCCAAACGGCTCTAAATATCCACTTGGAAATCCCACAAAAAGAGTATTTCAAAACTGCTCTATCAAAAGGAACGTTGACCTCTGTGAATTGAATGCACAGATCACAAAGAAGTTTCTGAGAGTTCTTCTCTCAAGTTTTCTGTGAAGAAATCCCGTTTCCAAAGAAGGCCTCCAAAAAGTACAAATATTCACTTCCAGATTCTACAAAAAGACTGTTTCAAAAAAGCTCTATCAAAAGAAAGTTTAAACTCTGTGAGTCGTAAGCACACATCACAAAGAAGTTTCTCAGAATCATTCTGTCTATTTTTTCTAACAAGATATTTCCTTTTCTAGCATAGGCCTCAAATGGAGCTAAATATCCACTTGGAAATACTACAAAAAGAGTTTCAAAACTGCTCTATCGAAAGAAAGGTTCAACTGTATGAGTTGAAAGCACACATCACAAAGAAGTTTCTGAGAGTTCTTCTGTCTAGTTTTGTATGAAGAAATCAGGTTTGAAATGAAGGCCACAAAGAGGTTCAAATATCCACTTGCAGATTCTACAAAAAGAGTGTTTCAAAACTGCTCTATCAAGAGAAATCTTCAACTCTGTGGGTTGAATGCAAATATCCCAAAGTAGTTTCTGACAATGCTTCTGTCTGGTTATTACGTGAAGATATATCCTTTTCTACCATAGGCCTCAAAGGGCTCTAAATAAACACTTCCAAAATCCACAAAAAGAGTGTTTCAAAACTGCTCTATCAATCAAAAGAAAGGTTAAACTCTGTAAGCTGAATGCACACATCACAAAGTAGTTTCTGAGAATGATTCTGTCTCGTTTTCCTATGAAGATATTTCCTATGAAGATATTTCCTTTCCTATCACAAGCCTCAAAGCGCTCTAAATATCTACTTGGAAATTCTACAGAAAGAGTATTTCAAAACTTCTCTCTCGAAGGGAAGGTTCAACTCTGTGAGTTGAATGCCCACATCACAAAGTAGTCTCTGAGAATTCTTCTGTTAAGTTTTATTTGAAGAAATCCCTTTACCAACGAACGCCACAAAAATTCCAAATATTCACTTGCAGATTCTCCAAAAAGAGTGTTTCAAAACTATTCTATAAAAAGAAAGTTTAACACTGTGAGATGAATGCACACATCTTAAAGTAGTTTCTGACAATCATTCTGTCTAGTTTTTCTATGAAGATATTGCCTTTTCTACCATAGGCCTCAAACGGCACTATATATCCACTTGGAAATTGTACAAAAAGAGCGTTTACAAACTGCTCTACCGAAAGGAAGGTTCAACACTGTGAGTTGAAAGCACACATCACAAAGATGTTTCTGAGAATTCTTCTGTTTAGTTTTATATGAAGAAACCACGTTTCAAACGAAGGTCACAAAGAGGTCCAAATATGCACGTGCAGATTCTACAAAAATAGTGTTTCAAAACTGCTTTATCAAGAGGAACGTTCAACTCTGTGAGTTCAATGCAAATGTCACAAAGAAGTTTCTGACAATGTTTCTGTCTAGGTTTTAGGTGAAGATATTTCCTTTTCTAACGTAGGCTGCCGAGCACTCTAAATATACACTTGCAAAATTCCACAAAAAGAGTGTTTCAAAACTGCACAATCAAAAGAAAGGTTAAACACAGTAAGCTGAATGCACACGGGACAAAGTAGTTTCTGAGAAGGATTCTGTCTTGTTTTTCTACGAAGATATGTCCTTCTCCAAAATAGGCCGCAAACCGCTCTAAATATTCACTTGGAATTTCTACAAAAAGAGTATTTCAAAACTGCTCTATCGAAAGGAAGGTTCAAACCTGTGAGTTGAATGCACATATCACAAAGAAGGTTCTGAGAATTCTTCTGTCAAGTTTTATGTGAAGAAACCCCGTTTCCAACGAAGGCCTCTTAAAAGTCCAAATATTCACTTGCAGATACTACAAAAACACTGTTTCAAAAGTGCTCTATCAAAAGAAAGTTTAAACTGTTTGAGTTGAACGCACACTTCACAAAGTAGTTTCTGAGAATCGTTATGTCAAGTTTTCCTAAGAAGATATTACCTTTTCAACCATAGGCCTCAAACAGCCCTAAATATCCACTTGGACATTCGACAGAAAGAGAGTTTCAAAACTCCTCTTTCGAAAGGCATGTTCCGTGAGTTGAACACAAACATCACAAGGTAGTTTCCGATAATCATTCTGTCTAATTTTTCTATGATGATAATGCCTTTTCTACCATTGGCTTCAAACGGCGCTAAATATCCACTTGGAAATTCTACAAAAAGAGTGTTTCAAAATTGCTCTATGAAGAGGAATGTCCAGCTCTGTAAGTTGAATGCAAATATCACAAATTAGTTTCTGACAATGCTTCTTTCTGGTTTTTATGTGAAGATATTTCCTTTTCTACCACAGGCCTCAAAGCGCTCTAAATATACACTTGCAAATTCCACAGAAAGAGTGTTTGAAAACTGCTGTATCAAAAGAAAGTTAAACTCTGTAAGCCGAATGCAGACATCACAAAGCAGTTTCTGAGAATGATTCTGTCTAATTTTTCTATGAAGATATTTCCTTTTCAACCACAAGCCTGAAACCGCTCTAAATATGCATTTGAAATTCTACAAAAAGAGTATATCAAAACTGCTCTATGGAAAGGAAGGTTAAACTCTGTGAGATGAATGCACTCATCACAAAGAAGTTTCTGAGAATTCTTTGGCAAAGTTTTATATGACAAAATCCCTTTTCCAAAGAAGGCCACAAAAATGTCCAAATATTCACTTGCAGATCCTCCAAAAAGTGTGTTTCAAAACTGCCCTATCAAAAGAAAGTTTGAACTCAGTGAGTTGAATGCACACATCACAAAGCAGTTTCTGAGAATCATTCTGTCTAGTTCTTCTATGAAGATATTGCCTTTTCTACCATAGACCTCAAACGGCGCTAAATATCCACTTGGAAATTCTACAAAAAGAGAGCTTCAAAACTGCTTTATCGAAAGGAATGTTAAAATATGTGAGTTGAAAGCACACATCACAAAGAAGTTTCTGAGAATTCTTCTGTCTAGTTTTATATGAAGAAATCACGTTTCAAACGAAGGCCCCAAAGAGGTCCAAATATACACCTGCAGATATTACAAAAAGAGTGTTTCAAAACTGCTCTATCATAAGAAAGGTTAAACTCTGTAAGCTTAATGCAAACATCACAAAGTAGTTTCTGAGAATGATTCTGTCTAGTTTTTCTATGAAGATATTTAATTTTCTGCCATAGGCCTCAAACCGCTCTAAATATACACTTGGAAATTCTACAAAAAGAGTATTTTAAAACTGCTCTATCGAAAGGAAGTTTTAACTCTGTGAGTTCAATGCACACATCAGAAAGAACTTTCTGAGAATTCTTCTGTCAAGTTTTAAAAGAAGAAAACCCGTTTCCAACAAAGGCCTCAAATATGTAAAAATATTAATTGGCACATTCAACAAAAAAGAGTGTTTCAAAACTGCTCCATCAAGAGGAACGTTCAACTCTGTGAGTTGAATGCAAATATCACAAAGTAGATTCTGACAATGCTTCTGTCAAGTTTTTATATGAAGATATTTCCTTTTCTACCATAGGATTCAAAGCGCTCTAAACATCCACTTGGAAATTCTACAAAAAGAGTGTTTCAAATCTGCTCTATCAAAAGGAAGGTTGCACTCTGAGAGTTGAATCCACACATCCCAAAGAATTTTCTGAGAATTCTTCTGTCTAGTTTTATACGAAGAAATCCTGTTTCCACTGAAGGCCTCAAAGAGTTCCAAACATACACTTGCAGAAACTACAAAAAGAGTGTTTCAAAACTGCTCTATCAAGAGGAATGTTCAACTCCGCGAGGTGAATGCAAACATCACAAAGCAGTTTCTGAGAATGCTTCTGTCTAGTTTTTATGTGAAGATATTTCCTTTTCTACCGTAGGCCTCGAAGTGATCTAAATATCCACTTGCAAACACTACAAAAGGGTGTTACAAAACTGCACTATCAAATGAAGGTTCACCTCTGTGAGTTGAGTACAGACATCACAAAGA, for input source: xxxxx.vcf.gz
at hts...@4.1.2/htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:887)
at hts...@4.1.2/htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:678)
at hts...@4.1.2/htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:640)
at hts...@4.1.2/htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:443)
at hts...@4.1.2/htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:384)
at hts...@4.1.2/htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:328)
at hts...@4.1.2/htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:48)
at org.igv/org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:69)
at org.igv/org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:43)
at hts...@4.1.2/htsjdk.tribble.TabixFeatureReader$FeatureIterator.readNextRecord(TabixFeatureReader.java:173)
at hts...@4.1.2/htsjdk.tribble.TabixFeatureReader$FeatureIterator.next(TabixFeatureReader.java:205)
at hts...@4.1.2/htsjdk.tribble.TabixFeatureReader$FeatureIterator.next(TabixFeatureReader.java:149)
at org.igv/org.broad.igv.feature.tribble.TribbleReaderWrapper.query(TribbleReaderWrapper.java:61)
at org.igv/org.broad.igv.track.TribbleFeatureSource$IndexedFeatureSource.getFeatures(TribbleFeatureSource.java:226)
at org.igv/org.broad.igv.track.FeatureTrack.loadFeatures(FeatureTrack.java:723)
at org.igv/org.broad.igv.track.FeatureTrack.load(FeatureTrack.java:676)
at org.igv/org.broad.igv.ui.IGV.lambda$repaint$16(IGV.java:2283)
at java.base/java.util.concurrent.CompletableFuture$AsyncRun.run(CompletableFuture.java:1804)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:840)

What is the issue with the allele?

Thanks,